The Potato Genome

Plant & Food Research and its previous incarnations have been involved in a multinational project to map the potato genome sequence. A first draft was issued in 2009, and this is now being used as the basis for attempts to improve yield, quality, nutritional value and disease resistance of potato varieties, and to reduce the time taken to breed new varieties, typically 10-12 years. The potato has four replicates of 12 chromosomes and the genome is estimated to be 840 million base pairs so it is a massive task, but recent progress has allowed Plant & Food to start to identify the genes controlling important characteristics in NZ cultivars that should be of value in improving colour, storage attributes, processing qualities, and resistance to pests and disease.

Dr Jeanne Jacobs is a scientist at Plant & Food, Lincoln and is a member of the international steering committee overseeing the project. A paper outlining progress is to be published in Nature soon.

Potato, a key member of the Solanaceae family, is a close relative of tomato, pepper and eggplant. It is the world’s third most important crop and the most important vegetable crop. Knowing the potato genome sequence (the genetic blueprint of how a potato plant grows and reproduces) should help to improve yield, quality, nutritional value and disease resistance of potato varieties. By identifying which bits of the genetic code hold the key to important traits, the project should fast track breeding programmes to produce improved cultivars, which takes 10 – 12 years using conventional breeding techniques.

The project was started in 2005 in the Netherlands where they wanted to determine the DNA sequence of the potato, but it was a very expensive exercise and the potato is a commodity crop so there were no big dollars to drive it. Dutch researchers looked for partners, and because of the reputation of the genetics and biotechnology research at Lincoln, they invited Dr Jeanne Jacobs to become involved. Other partners initially included the USA, Scotland, Ireland, and China. Later others joined and there are currently 27 research organisations in 14 countries that have participated.

The first draft sequence of a baseline variety was issued in 2009. Subsequently some additions and changes to the research programme were made as new methods became available. At present all the available information is in a database. Some of the data are available to the public, all of the data are available to the partners in the consortium. The flagship paper is soon to be published in Nature and then all will be in the public domain and the whole scientific community will have access to it.

New Zealand has been a lead partner in the project, has put a considerable investment into it and has had an important role in making it successful. Dr Jacobs is a member of the international steering committee overseeing the project, and says that the task the partners face is huge and very complicated.

“The potato has four sets of 12 chromosomes and the genome is estimated to be 840 million base pairs of nucleotides, so sorting out the sequence is a massive project. We have been puzzling over that and trying to make sense of how they all work and what causes what,” she says.

“So we chopped all the DNA of a particular cultivar up into small bits to determine the sequence of nucleotides and what order and numbers they are in, and then pieced it all together again. That has given us a baseline that we can now compare with the different potato materials we grow for eating and for processing into chips and crisps, and also material that is used in other countries for industrial processing.”

Essentially Plant & Food Research can now start to determine which genes of interest are available in different NZ cultivars, whether particular genes are switched on or off, how potato colour is expressed in the DNA, and which sequences confer disease resistance, better storage properties or enhanced processing characteristics.

“Now that we have a reference genome sequence (a ‘baseline’) we are able to rapidly resequence– find where the differences are from the baseline genome sequence – elite NZ cultivars. For example we have already done this for four cultivars in a few months and we intend to do more in the near future. This helps us to determine where the sequences are that control the characteristics we want. That makes it quicker to select material that is valuable,” says Dr Jacobs.

“Now we are starting to make the link between what we can see and measure in tubers and what we see in the DNA, and we are only just scratching the surface on that. For instance we have a line that is very good for processing purposes – what can we measure on that characteristic and how does it relate back to the genes in that material?”

For New Zealand growers and processors the benefits of the genome work will start to accrue through new breeding approaches. It will help Dr Jacobs and other researchers to identify cultivars that could be crossed or bred from to get better processing characteristics and disease resistance. “For example, the tomato-potato psyllid causes many potatoes to be rejected for processing and is becoming a tremendous cost to the industry, especially in the North Island”, says Dr Jacobs.

“If we can find genes that would potentially give resistance to this pest or resistance to the bacterium that it transmits then we could very quickly implement that in the breeding programme and it would cut development time. The problem with disease resistance is that you can’t see it in the same way that you can see, say, purple skin or flesh. So you have to do repeated multi-year trials where you expose the material to the pathogen and there is a lot of environment variation and so it is often a very cumbersome process,” she says.

“However, if we can predict with say, 95% probability that certain lines are going to be resistant, then we speed that process considerably. So the biggest gains are to be made with traits that are not visible or obvious.”

A spin-off from the project is a silicon chip that has markers on it based on the 2009 draft of the sequence. “Researchers in the USA found many tiny differences between the nucleotides in genes and sometimes these differences affect the way a gene functions and will cause a different outcome”, says Dr Jacobs. The silicon chips have 10,000 spots on them where the tiny differences are, and these are in genes that researchers have some idea of their function. The technique allows scientists to look very quickly at the genetic material variation by taking a “helicopter view” where they see the highlights, and that is sufficient to give a good indication of what material merits further study.

Dr Jacobs believes that the project is leading to a better understanding of the DNA of material in NZ potato cultivars. The main traits of interest are storage and processing quality and disease resistance.

“Factories need to process potatoes all year round so tubers get stored in the cold, and if you take them out of the cold they often fry and chip very badly because at cold temperatures the starches get converted into sugars, and those sugars give the chips and crisps a dark brown burnt colour and a bitter taste that you don’t want,” she says.

“The material can sometimes be restored by holding it at room temperature for a while before you chip or fry it, but not every line does that and the reason why it is becoming an increasing problem is that anti-sprouting chemicals can no longer be used, and so to avoid sprouting during long-term storage potatoes have to be stored colder. Unfortunately the process of cold-induced sweetening is worse at lower temperatures so we have to strike a balance between a cold enough temperature to prevent them from sprouting before they go to processing and producing too much sugar and completely sweetening up.”

“Resistance to pests and diseases is always important, and then there are niche markets for different colours, and for more waxy potatoes or orange fleshed potatoes, there are always changes in what people want.”

“So the targets I would look at are healthy potatoes, good processing potatoes, good yields even under water stress or heat stress with climate change and perhaps with more UV. We need to anticipate the future because from the time a potato breeder makes a cross, to the point where they achieve a cultivar available in commercial quantities for consumers or processors, is currently 12 years as a minimum, so anything we can do to speed up that process will be an enormous gain.”